I've never understood the problem some people have with hate crimes. Don't we already have plenty of crimes where the only differentiator is mental state or intent? Hard to see how a hate crime classification is any different than, say, Murder 1 versus Murder 2.
I would assume it's a perceived sense of lack of fairness in the sentencing; to be clear, I share your position on hate crimes. They exist for the same reason that we have both Murder and Manslaughter charges, because our system of law considers intent as part of the sentencing.
But it is not hard to see how some would view such laws as unfair. Intent can be difficult to prove and it requires interpretation; if you believe in clear cut and easily understandable laws, then naturally Hate Crimes and other such laws probably seem like a bad idea, and I get why that is frustrating and even intimidating with how fast gossip can travel. The system itself is built with release valves, but it's likely not much comfort for the wrongly accused.
I think that's a separate problem, however, which is just exacerbated by perceptions of laws like Hate Crimes as opposed to being caused by the laws themselves.